File Changes for angie

v293_preview2 to v293_base (2013-12-02 to 2013-12-09) v293

• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 3, context: html, text, full: html, text
    Fixing a dependency that broke parallel make (thanks Jonathan for finding!) and using ${MAKE} instead of make so that parallel make won't warn about 'jobserver unavailable'.
  • lines changed 1, context: html, text, full: html, text
    Adding a missing dependency (cgi depends on edwLib) in hopes that it prevents sporadic errors from ld reading nonsense.
• src/hg/hgVai/hgVai.c
  • lines changed 47, context: html, text, full: html, text
    Added a couple ENCODE Regulation summary tracks to hgVai. refs #11461
  • lines changed 3, context: html, text, full: html, text
    Finally added hgTrackUi links for tracks offered by hgVai. Thanks for the prod, Jonathan! refs #11461
  • lines changed 47, context: html, text, full: html, text
    Revert "Added a couple ENCODE Regulation summary tracks to hgVai. refs #11461"This reverts commit c65b04d176ad125c1eddd777fb8befd481bdba2c.
    I decided that hgVai's support for regulatory tracks is not sufficient to roll
    out to the RR because annoFormatVep isn't yet smart enough to add regulatory
    consequence SO term (regulatory_region_variant) when one or more of these overlap.
    Also, there really should be some filtering - I suspect the false positive rate
    will be too high otherwise because the Tfbs cover 1/8th of the genome. The next
    release to the RR is not until Jan. 21, more than a month from now. I'll bring
    this back after the v293 build is tagged.
    refs #11461
    
• src/lib/annoGratorQuery.c
  • lines changed 21, context: html, text, full: html, text
    In annoGratorQueryExecute, if we're searching a specific region andthe primary source's first item comes from some later chromosome,
    that simply means that the primary source has no items on the
    specified chrom. So instead of passing it to the grators, just
    quit. Also when searching a specific region, if there are no rows
    from the primary source, add a comment to the output(s).
    fixes #12278